Installation

container (preferred)

We recommend using the Neurodocker Docker image, which can be access through Docker or Singularity.

docker run --rm repronim/neurodocker:latest --help

Note: Some tools require an interactive input during installation (e.g. FSL). This can either be handled using the Neurodocker –yes option (see examples -> FSL) or running the container interactively will also allow to answer this question:

docker run -i --rm

Alternatively, a singularity container:

singularity run docker://repronim/neurodocker:latest --help

Note: The version tag latest is a moving target and points to the latest stable release.

repronim/neurodocker:latest -> latest release (0.9.4 now)
repronim/neurodocker:master -> master branch
repronim/neurodocker:0.9.4
repronim/neurodocker:0.9.2
repronim/neurodocker:0.9.1
repronim/neurodocker:0.9.0
repronim/neurodocker:0.8.0
repronim/neurodocker:0.7.0
...

pip

Neurodocker can also be installed with pip. This is useful if you want to use the Neurodocker Python API. Python 3.7 or newer is required.

python -m pip install neurodocker
neurodocker --help

conda

We recommend using a virtual environment or a conda environment. In order to create a new conda environment and install Neurodocker:

conda create -n neurodocker python=3.9
conda activate neurodocker
python -m pip install neurodocker
neurodocker --help